Complete genome sequencing and genetic characterization of porcine sapovirus genogroup (G) X and GXI: GVI, GVII, GX, and GXI sapoviruses share common genomic features and form a unique porcine SaV clade

Infect Genet Evol. 2019 Nov;75:103959. doi: 10.1016/j.meegid.2019.103959. Epub 2019 Jul 9.

Abstract

Sapoviruses (SaVs) are enteric viruses belonging to the family Caliciviridae that infect humans and animals, including pigs. To date, SaVs have been classified into 19 genogroups (G) based on complete VP1 sequences; however, complete genome sequences of some SaV Gs are not yet available. In this study, we determined the full genome sequences of four SaVs (two GX and two GXI SaVs) and analyzed them together with those of other SaVs. The complete genome sequences of GX and GXI SaVs, excluding the poly(A) tails, were 7124, 7142, 7170, and 7179 nucleotides, which were shorter than those of other SaVs, except for porcine GVI and GVII viruses. Genetic characterization revealed that GX SaVs and GXI SaVs shared common features with GVI and GVII viruses, such as the first 10 amino acid residues in the ORF1 coding region, a shorter ORF1 than that of the other genogroups, and the predicted secondary structure of the 5' end of the genome and the starting region of non-structural protein/structural protein junction. Phylogenetic analyses showed that GX and GXI SaVs branched with porcine GVI, GVII, and GIX SaVs and formed a clade consisting of only porcine SaVs. These findings suggest that porcine GX and GXI SaVs together with porcine GVI, GVII, and possibly GIX SaVs, evolved from a common ancestor in the porcine population.

Keywords: Complete genome sequencing; Genogroup; Genotype; Pig; Sapovirus.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Base Sequence
  • Feces / virology
  • Genome, Viral
  • Genotype
  • Nucleic Acid Conformation
  • Phylogeny
  • RNA, Viral / genetics
  • Sapovirus / classification
  • Sapovirus / genetics*
  • Swine / virology*

Substances

  • RNA, Viral